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<h2>Description</h2>
<p>
perform streamlines tracking.
</p>
<p class=indented><strong>syntax:</strong> &nbsp; &nbsp; streamtrack [ options ] type source tracks </p>
<h2>Arguments</h2>
<table class=args>
<tr><td><b>type</b></td>
<td>the type of streamlines tracking to be performed. Allowed types are DT_STREAM, SD_STREAM, SD_PROB.</td></tr>
<tr><td><b>source</b></td>
<td>the image containing the source data. The type of data required depends on the type of tracking as set in the preceeding argument. For DT methods, the base DWI are needed. For SD methods, the SH harmonic coefficients of the FOD are needed.</td></tr>
<tr><td><b>tracks</b></td>
<td>the output file containing the tracks generated.</td></tr>
</table>
<h2>Options</h2>
<table class=args>
<tr><td><b>-seed</b>&nbsp;<i>spec</i></td>
<td>specify the seed region of interest.
<table class=opts>
<tr><td><i>spec</i></td>
<td>specifies the parameters necessary to define the ROI. This should be either the path to a binary mask image, or a comma-separated list of 4 floating-point values, specifying the [x,y,z] coordinates of the centre and radius of a spherical ROI.</td></tr>
</table></td></tr>
<tr><td><b>-include</b>&nbsp;<i>spec</i></td>
<td>specify an inclusion region of interest, in the same format as the seed region. Only tracks that enter all such inclusion ROI will be produced.
<table class=opts>
<tr><td><i>spec</i></td>
<td>specifies the parameters necessary to define the ROI.</td></tr>
</table></td></tr>
<tr><td><b>-exclude</b>&nbsp;<i>spec</i></td>
<td>specify an exclusion region of interest, in the same format as the seed region. Only tracks that enter any such exclusion ROI will be discarded.
<table class=opts>
<tr><td><i>spec</i></td>
<td>specifies the parameters necessary to define the ROI.</td></tr>
</table></td></tr>
<tr><td><b>-mask</b>&nbsp;<i>spec</i></td>
<td>specify a mask region of interest, in the same format as the seed region. Tracks will be terminated when they leave any such ROI.
<table class=opts>
<tr><td><i>spec</i></td>
<td>specifies the parameters necessary to define the ROI.</td></tr>
</table></td></tr>
<tr><td><b>-step</b>&nbsp;<i>size</i></td>
<td>set the step size of the algorithm.
<table class=opts>
<tr><td><i>size</i></td>
<td>the step size to use in mm (default is 0.2 mm).</td></tr>
</table></td></tr>
<tr><td><b>-curvature</b>&nbsp;<i>radius</i></td>
<td>set the minimum radius of curvature (default is 2 mm for DT_STREAM, 0 for SD_STREAM, 1 mm for SD_PROB and DT_PROB).
<table class=opts>
<tr><td><i>radius</i></td>
<td>the radius of curvature to use in mm.</td></tr>
</table></td></tr>
<tr><td><b>-grad</b>&nbsp;<i>scheme</i></td>
<td>specify the diffusion encoding scheme (may be required for DT_STREAM, ignored otherwise).
<table class=opts>
<tr><td><i>scheme</i></td>
<td>the DW gradient file.</td></tr>
</table></td></tr>
<tr><td><b>-number</b>&nbsp;<i>tracks</i></td>
<td>set the number of tracks to calculate (default is 100 for *_STREAM methods, 1000 for *_PROB methods).
<table class=opts>
<tr><td><i>tracks</i></td>
<td>the number of tracks.</td></tr>
</table></td></tr>
<tr><td><b>-length</b>&nbsp;<i>value</i></td>
<td>set the maximum length of any track.
<table class=opts>
<tr><td><i>value</i></td>
<td>the maximum length to use in mm (default is 200 mm).</td></tr>
</table></td></tr>
<tr><td><b>-minlength</b>&nbsp;<i>value</i></td>
<td>set the minimum length of any track.
<table class=opts>
<tr><td><i>value</i></td>
<td>the minimum length to use in mm (default is 10 mm).</td></tr>
</table></td></tr>
<tr><td><b>-cutoff</b>&nbsp;<i>value</i></td>
<td>set the FA or FOD amplitude cutoff for terminating tracks (default is 0.1).
<table class=opts>
<tr><td><i>value</i></td>
<td>the cutoff to use.</td></tr>
</table></td></tr>
<tr><td><b>-initcutoff</b>&nbsp;<i>value</i></td>
<td>set the minimum FA or FOD amplitude for initiating tracks (default is twice the normal cutoff).
<table class=opts>
<tr><td><i>value</i></td>
<td>the initial cutoff to use.</td></tr>
</table></td></tr>
<tr><td><b>-trials</b>&nbsp;<i>number</i></td>
<td>set the maximum number of sampling trials at each point (only used for probabilistic tracking).
<table class=opts>
<tr><td><i>number</i></td>
<td>the number of trials.</td></tr>
</table></td></tr>
<tr><td><b>-unidirectional</b></td>
<td>track from the seed point in one direction only (default is to track in both directions).</td></tr>
<tr><td><b>-initdirection</b>&nbsp;<i>dir</i></td>
<td>specify an initial direction for the tracking.
<table class=opts>
<tr><td><i>dir</i></td>
<td>the vector specifying the initial direction.</td></tr>
</table></td></tr>
<tr><td><b>-noprecomputed</b></td>
<td>do NOT pre-compute legendre polynomial values. Warning: this will slow down the algorithm by a factor of approximately 4.</td></tr>
<tr><td><b>-info</b></td>
<td>display information messages.</td></tr>
<tr><td><b>-quiet</b></td>
<td>do not display information messages or progress status.</td></tr>
<tr><td><b>-debug</b></td>
<td>display debugging messages.</td></tr>
<tr><td><b>-help</b></td>
<td>display this information page and exit.</td></tr>
<tr><td><b>-version</b></td>
<td>display version information and exit.</td></tr>
</table>
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